Ecoimmunology affords us the ability to better understand immunological processes through consideration of external factors, such as the thermal microenvironment. This consideration is imperative when examining the immunological processes of ectothermic organisms like reptiles. Reptiles uniquely rely heavily on their innate immune function but remain poorly understood in immunological studies. In this study, we examined innate immunity in two zoo‐housed tortoise species, the Indian star tortoise (Geochelone elegans, Schoepff, 1795) and northern spider tortoise (Pyxis arachnoides brygooi, Vuillemin & Domergue, 1972). Bacterial killing assays (BKAs) were optimized and used to assess the monthly immunocompetence of these tortoises to three different bacteria: Escherichia coli, Salmonella enterica, and Staphylococcus aureus. We evaluated differences in blood biochemistry values (lactate and glucose) among months and species as well as fecal corticosterone (CORT) between species. Lastly, we examined the potential influences of individual thermal microenvironments on bactericidal ability. Both G. elegans and P. a. brygooi demonstrated immunocompetence against all bacterial challenges, but only bactericidal ability against E. coli varied over months. Optimal BKA serum dilutions, blood glucose levels, and fecal CORT concentrations differed between the two species. Finally, there was evidence that the thermal microenvironment influenced the tortoises’ bactericidal ability against E. coli. Through use of nonmodel organisms, such as tortoises, we are given insight into the inner workings of innate immunity and a better understanding of the complexities of the vertebrate immune system.